A new species of parasitic copepod, Caligus fajerae n. sp. (Caligidae), is described from Scomberomorus sierra Jordan & Starks (Scombridae) caught off the northwestern coast of Mexico. The new species morphologically resembles Caligus cybii Bassett-Smith, 1898, Caligus kanagurta Pillai, 1961, Caligus pelamydis Krøyer, 1863 and Caligus robustus Bassett-Smith, 1898, all of which have been reported from scombrid hosts. Caligus fajerae n. sp. differs from these species by having spinules on the abdomen and caudal ramus, two processes on the proximal antennulary segment, fine striations on the claw of the antenna and maxilliped, a stouter and more recurved maxillulary dentiform process, shorter tines on the sternal furca, two additional patches of spinules on the distal endopodal segment of leg 2, a sclerotised lobe on the anteromedian surface of the leg 3 protopod and serrations on both margins of the first exopodal spine of leg 3. Analysis of the DNA sequences of the mitochondrial cytochrome c oxidase subunit 1 gene for Caligus fajerae n. sp. and 28 congeners, including C. pelamydis and C. robustus, showed that the new species grouped with Caligus belones Krøyer, 1863 (with 20% divergence), a species known to occur predominantly on needlefishes. Caligus fajerae n. sp. is the fifth species of Caligus reported from S. sierra. An updated host-parasite list for Caligus spp. on scombrids is provided.